Comment 2 for bug 1356892

I have tested this in 15.04 Beta 2 (fully updated) and this issue happens not because of 2 Caja windows open but when a window is not in focus.

1. Open any window (Caja, Control Centre etc)
2. Left Click outside the window (window will then not be in focus)
3. Hover the mouse cursor over the 3 buttons to the right and the left window control button
4. Buttons disappear when hovered over when the window is not in focus.

I've added an image so you can see. The buttons are not merely faded when hovered but the graphics do actually disappear.